samtools sort - Githubissues

vpc-ccg / sedef

Identification of segmental duplications in the genome

MIT License

26 stars 8 forks source link

samtools sort #9

Closed calkan closed 5 years ago

calkan commented 5 years ago

Currently it sorts the entire BAM (and hopefully soon, CRAM) file, then extracts the discordant. Do it other way around to reduce the sorting time. This is also easy:

Calculate min/max (as in issue #8)
When doing samtools view, pipe to awk command to filter out the concordants, then pipe to sort.

calkan commented 5 years ago

oops, wrong repo